White light-emitting diodes (WLEDs) with quantum dots (QDs) and phosphor have attracted tremendous attentions due to their excellent color rendering ability. In the packaging process, QDs layer and phosphor-silicone layer tend to be separated to reduce the reabsorption losses, and to maintain the stability of QDs surface ligands. This study investigated the packaging sequence between QDs and phosphor on the optical and thermal performances of WLEDs. The output optical power and PL spectra were measured and analyzed, and the temperature fields were simulated and validated experimentally by infrared thermal imager. It was found that when driven by 60 mA, the QDs-on-phosphor type WLEDs achieved luminous efficiency (LE) of 110 lm/W, with color rendering index (CRI) of Ra = 92 and R9 = 80, while the phosphor-on-QDs type WLEDs demonstrated lower LE of 68 lm/W, with Ra = 57 and R9 = 24. Moreover, the QDs-on-phosphor type WLEDs generated less heat than that of another, consequently the highest temperature in the QDs-on-phosphor type was lower than another, and the temperature difference can reach 12.3°C. Therefore, in terms of packaging sequence, the QDs-on-phosphor type is an optimal packaging architecture for higher optical efficiency, better color rendering ability and lower device temperature.